Variant report

Variant	rs6509983
Chromosome Location	chr19:56616426-56616427
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr19:56616348-56617013	SK-N-SH	brain:	n/a	chr19:56616634-56616652 chr19:56616637-56616650 chr19:56616944-56616957 chr19:56616992-56617005 chr19:56616938-56616951 chr19:56616577-56616590 chr19:56616635-56616651 chr19:56616636-56616657 chr19:56616943-56616951
2	MAX	chr19:56616395-56616983	A549	lung:	n/a	chr19:56616951-56616961
3	CTCF	chr19:56616383-56616956	MCF-7	breast:	n/a	chr19:56616634-56616652 chr19:56616637-56616650 chr19:56616938-56616951 chr19:56616577-56616590 chr19:56616635-56616651 chr19:56616636-56616657 chr19:56616943-56616951
4	MAX	chr19:56616380-56617088	ECC-1	luminal epithelium:	n/a	chr19:56616951-56616961
5	CTCF	chr19:56616395-56616804	H1-hESC	embryonic stem cell:	n/a	chr19:56616634-56616652 chr19:56616637-56616650 chr19:56616577-56616590 chr19:56616635-56616651 chr19:56616636-56616657
6	RAD21	chr19:56616421-56616921	ECC-1	luminal epithelium:	n/a	chr19:56616580-56616594 chr19:56616636-56616650 chr19:56616635-56616654
7	RAD21	chr19:56616394-56617070	ECC-1	luminal epithelium:	n/a	chr19:56616580-56616594 chr19:56616988-56617002 chr19:56616636-56616650 chr19:56616635-56616654 chr19:56616941-56616955
8	TCF12	chr19:56616380-56617171	ECC-1	luminal epithelium:	n/a	n/a
9	MAX	chr19:56616386-56616890	H1-hESC	embryonic stem cell:	n/a	n/a
10	MAX	chr19:56616409-56616878	A549	lung:	n/a	n/a
11	POLR2A	chr19:56616357-56618960	PANC-1	pancreas:	n/a	n/a
12	MAX	chr19:56616386-56617055	HepG2	liver:	n/a	chr19:56616951-56616961
13	POLR2A	chr19:56616410-56617096	PANC-1	pancreas:	n/a	n/a
14	CTCF	chr19:56616280-56616430	HMEC	breast:	n/a	n/a
15	YY1	chr19:56616373-56616805	HepG2	liver:	n/a	n/a
16	RAD21	chr19:56616379-56616880	A549	lung:	n/a	chr19:56616580-56616594 chr19:56616636-56616650 chr19:56616635-56616654
17	MXI1	chr19:56616421-56617008	IMR90	lung:	n/a	n/a
18	RAD21	chr19:56616416-56616878	A549	lung:	n/a	chr19:56616580-56616594 chr19:56616636-56616650 chr19:56616635-56616654
19	RAD21	chr19:56616342-56616897	H1-hESC	embryonic stem cell:	n/a	chr19:56616580-56616594 chr19:56616636-56616650 chr19:56616635-56616654
20	SRF	chr19:56616419-56617131	ECC-1	luminal epithelium:	n/a	chr19:56616752-56616769
21	RAD21	chr19:56616359-56616909	HepG2	liver:	n/a	chr19:56616580-56616594 chr19:56616636-56616650 chr19:56616635-56616654

No.	Distal block	Cell Line	Cell type
1	chr19:56615193..56619302-chr19:56653183..56656350,4	MCF-7	breast:
2	chr19:56587637..56588335-chr19:56616080..56616703,2	MCF-7	breast:
3	chr19:56616140..56616760-chr19:56683418..56683934,2	MCF-7	breast:
4	chr19:56612599..56616950-chr19:56825214..56827593,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000223060	TF binding region
ZNF787	TF binding region
ENSG00000167685	Chromatin interaction
ENSG00000131848	Chromatin interaction
ENSG00000267549	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11673628	0.83[AFR][1000 genomes]
rs12980196	0.82[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs35766803	0.85[AFR][1000 genomes]
rs513915	0.89[ASN][1000 genomes]
rs514916	0.87[ASN][1000 genomes]
rs578901	0.84[ASN][1000 genomes]
rs606882	0.82[EUR][1000 genomes]
rs7253923	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7254130	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7254265	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7260339	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs744309	0.90[AMR][1000 genomes]
rs8103698	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1056598	chr19:56331762-56703428	Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
2	nsv1064371	chr19:56418215-56842450	ZNF genes & repeats Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
3	nsv1057316	chr19:56418215-56849458	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
4	nsv580354	chr19:56505685-56723492	Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
5	nsv833883	chr19:56512601-56640089	Strong transcription Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
6	nsv523651	chr19:56537528-56707048	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
7	nsv1057820	chr19:56555942-56720262	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
8	nsv528998	chr19:56578238-56707048	Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
9	nsv912512	chr19:56592286-56636759	Enhancers Genic enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
10	nsv517365	chr19:56592286-56674548	Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
11	nsv912513	chr19:56592286-56685463	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
12	nsv521744	chr19:56592286-56686953	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
13	nsv912514	chr19:56596815-56636759	Flanking Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
14	nsv912515	chr19:56598829-56623710	Weak transcription Genic enhancers Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
15	nsv912516	chr19:56601298-56981382	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	93 gene(s)	inside rSNPs	diseases
16	esv1809307	chr19:56604027-56633623	Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
17	esv1811581	chr19:56609313-56631618	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
18	esv1824038	chr19:56610449-56636632	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56592600-56620000	Weak transcription	HSMMtube	muscle
2	chr19:56592800-56622600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr19:56593000-56616600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr19:56593000-56616800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr19:56593000-56631200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr19:56594800-56616800	Weak transcription	HUVEC	blood vessel
7	chr19:56597200-56619400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr19:56600000-56619000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr19:56600800-56616800	Weak transcription	Small Intestine	intestine
10	chr19:56602800-56620000	Weak transcription	NH-A	brain
11	chr19:56603000-56616600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr19:56603200-56619800	Weak transcription	NHDF-Ad	bronchial
13	chr19:56603800-56616800	Weak transcription	Psoas Muscle	Psoas
14	chr19:56604800-56616800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr19:56605200-56617000	Weak transcription	Brain Angular Gyrus	brain
16	chr19:56605200-56619800	Weak transcription	HSMM	muscle
17	chr19:56605200-56620000	Weak transcription	Fetal Kidney	kidney
18	chr19:56606400-56616600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr19:56608200-56618600	ZNF genes & repeats	Brain Germinal Matrix	brain
20	chr19:56609600-56619600	Weak transcription	Fetal Heart	heart
21	chr19:56611400-56617000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr19:56611600-56616800	Strong transcription	Fetal Intestine Small	intestine
23	chr19:56613200-56616800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr19:56613200-56620000	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr19:56613400-56616800	Weak transcription	Osteobl	bone
26	chr19:56613600-56619800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr19:56613800-56616800	Weak transcription	Fetal Lung	lung
28	chr19:56614000-56616800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr19:56614000-56616800	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr19:56614000-56616800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr19:56614200-56616600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr19:56614200-56616600	Weak transcription	Hela-S3	cervix
33	chr19:56614200-56616600	Weak transcription	HMEC	breast
34	chr19:56614200-56616800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr19:56614200-56616800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr19:56614400-56616600	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr19:56614400-56616600	Weak transcription	Brain Hippocampus Middle	brain
38	chr19:56614400-56616600	Weak transcription	GM12878-XiMat	blood
39	chr19:56614400-56616800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr19:56614600-56616600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr19:56614600-56616600	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr19:56614600-56616800	Weak transcription	Fetal Intestine Large	intestine
43	chr19:56614800-56616600	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr19:56615000-56616600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr19:56615000-56616600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr19:56615000-56616600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr19:56615000-56616600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr19:56615000-56616600	Weak transcription	Placenta	Placenta
49	chr19:56615000-56616600	Weak transcription	Fetal Thymus	thymus
50	chr19:56615000-56616600	Weak transcription	Ovary	ovary

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